Microbiome and multi-omics snakemake workflows
General overview
The workflows displayed in this document define the snakemake rules in a DAG (directed acyclic graph) format. You may find a link to the interactive snakemake HTML report in some workflow. The link will enable you to explore the workflow and associated statistics. While exploring the interactive workflow, you can close the left bar (the overlap) to get a more expansive display view.
IMAP-PART 01
Software requirement for microbiome data analysis
Explore the IMAP-PART 01 interactive snakemake report (if available) here.
IMAP-PART 02
Exploring and profiling SRA sample metadata
Explore the IMAP-PART 02 interactive snakemake report (if available) here.
IMAP-PART 03
Downloading SRA FastQ reads using fasterq-dump
Explore the IMAP-PART 03 interactive snakemake report (if available) here.
IMAP-PART 04
Quality Control of Sequencing Reads
Explore the IMAP-PART 04 interactive snakemake report (if available) here.
IMAP-PART 05
Microbial profiling with MOTHUR pipeline
Explore the IMAP-PART 05 interactive snakemake report (if available) here.
IMAP-PART 06
Microbial profiling with QIIME2 pipeline
Explore the IMAP-PART 06 interactive snakemake report (if available) here.
IMAP-PART 07
Data processing for download analysis
Explore the IMAP-PART 07 interactive snakemake report (if available) here.
IMAP-PART 08
Data exploration and visualization
Explore the IMAP-PART 08 interactive snakemake report (if available) here.
Multi-Omics data analysis
…BRIEF INTRO IN PROGRESS…
Citation
Please consider citing the iMAP article[1] if you find any part of the IMAP practical user guides helpful in your microbiome data analysis.
References
Appendix
Project main tree
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├── LICENSE
├── README.md
├── config
│  ├── config.yml
│  ├── pbs
│  │  ├── cluster.yaml
│  │  └── config.yaml
│  ├── samples.tsv
│  ├── slurm
│  │  ├── cluster.yaml
│  │  └── config.yaml
│  └── units.tsv
├── dags
│  ├── rulegraph.png
│  └── rulegraph.svg
├── images
│  ├── bioinformatics.png
│  ├── bkgd.png
│  ├── imap.png
│  ├── imap_part01.svg
│  ├── imap_part02.svg
│  ├── imap_part03.svg
│  ├── imap_part04.svg
│  ├── imap_part05.svg
│  ├── imap_part06.svg
│  ├── imap_part07.svg
│  ├── imap_part08.svg
│  ├── rulegraph.png
│  └── smkreport
│  └── screenshot.png
├── index.Rmd
├── library
│  ├── apa.csl
│  ├── export.bib
│  ├── imap.bib
│  └── references.bib
├── report.html
├── results
│  └── project_tree.txt
├── smk.css
├── styles.css
└── workflow
├── Snakefile
├── envs
│  ├── environment.yml
│  ├── mothur.yml
│  └── qiime220232.yml
├── report
│  ├── biobakery.rst
│  ├── explore.rst
│  ├── imap.rst
│  ├── mothur.rst
│  ├── process.rst
│  ├── qiime2.rst
│  ├── readqc.rst
│  ├── rsmkrpt.rst
│  ├── software.rst
│  ├── sracache.rst
│  ├── srametadata.rst
│  ├── srareads.rst
│  └── workflow.rst
├── rules
│  ├── render_index.smk
│  ├── report.smk
│  ├── rmd_report.smk
│  └── rules_dag.smk
└── scripts
├── README.md
├── files4smk_report.sh
├── render.R
├── rules_dag.sh
├── smk_html_report.sh
└── tree.sh
14 directories, 60 files
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